If there were any lingering doubts about the urgency of the comprehensive repairs to the tracks at Pennsylvania Station in Manhattan, the derailment of another commuter train on Thursday night should have quashed them.

The derailment, the third since late March at Penn Station, happened at a crucial junction that is scheduled to be closed and replaced this summer. None of the 180 passengers and crew members aboard the New Jersey Transit train that came off the tracks was injured, but the derailment underscored how hazardous the condition of the tracks there has become.

The derailment occurred at a section where trains entering the station from a tunnel under the Hudson River are switched onto one of the 21 tracks leading to platforms beneath Penn Station’s main concourse. Officials of Amtrak, which owns and operates the station, have admitted that the junction, which is known as an interlocking, is long overdue for an overhaul.

“Last night just reinforced the need to go in and do the work very quickly and in a focused way,” said Scot Naparstek, the chief operating officer of Amtrak.

But their plan for making those repairs — and the nearly summer-long disruption it will cause — has drawn harsh criticism from the governors of New York and New Jersey and other elected officials. The work, scheduled to start on Monday and continue until early September, will require New Jersey Transit, the Long Island Rail Road and Amtrak — the three railroads that share Penn Station — to divert dozens of daily trains that carry thousands of passengers.

Gov. Andrew M. Cuomo of New York has warned of a “summer of hell” and threatened to withhold payments to Amtrak for the Long Island Rail Road’s use of Penn Station. Mr. Cuomo and other elected officials have questioned whether Amtrak is capable of maintaining the station, the busiest in the nation.

Amtrak officials have said that the recent derailments spurred them to accelerate the schedule of track repairs. They said those repairs would include tearing out some sections entirely, including parts of the area where Thursday’s derailment occurred, known as “A interlocking.”

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Amtrak workers on the tracks beneath the station on Friday.CreditBrendan McDermid/Reuters

Mr. Naparstek said he did not yet know what had caused the latest derailment. But he said Amtrak planned to focus first on the interlocking because that is where it had seen “a degradation of reliability.”

Two previous derailments, in late March and early April, occurred nearby, Mr. Naparstek said. They were “not in the same exact area on the same switches, but they were all on A interlocking,” he said. “A interlocking is the area that needs the most attention.”

The low-speed derailment Thursday night occurred at the 89th switch that trains arriving from New Jersey encounter, he said. The front wheels of the first passenger car of a train arriving from the Jersey Shore left the rails of Track 10 shortly after 9 p.m., stranding its passengers for about 90 minutes and disrupting New Jersey Transit service for more than two and a half hours.

In the first derailment this year, in late March, an Amtrak train sideswiped a New Jersey Transit train on Track 6. No one was injured, but the accident shut down Penn Station for most of the day.

Two weeks later, in early April, an inbound New Jersey Transit train derailed at slow speed on Track 9, injuring five people and forcing the diversion of trains from New Jersey to Hoboken Terminal for several days, upending the lives of many travelers who complained of commutes that stretched to hours.

Some commuters wondered aloud on Thursday how and why such problems have recurred.

“You really didn’t check anything else when you were down there?” asked Kyle Holthus, rhetorically addressing the Amtrak workers who dealt with the previous derailments. “It drives me bonkers,” Mr. Holthus, 38, added as he awaited a train home to Bloomfield, N.J.

A regular rider of early-morning trains to Penn Station, he said he avoids rush-hour trains home, preferring to “find a good place to read my book and wait for the craziness to stop.” As for how he will cope with the reduced service starting next week, he said, “I’m kind of in a wait-and-see pattern.”

This derailment was less disruptive than the previous ones, Mr. Naparstek said, “because the infrastructure damage to the tracks and other components was relatively minor, which is why, fortunately, we were able to return the station to pretty much to full capacity.”

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A New Jersey Transit train on the tracks beneath the station in May.CreditSeth Wenig/Associated Press

The passengers had to evacuate to a rescue train that eventually delivered them to a platform. Service was restored close to midnight, and the trains were running on time again by 7 a.m., a spokesman for New Jersey Transit said. Nancy Snyder, a spokeswoman for the railroad, said that New Jersey Transit was awaiting word from Amtrak on what had caused the derailment.

Gov. Chris Christie of New Jersey said in a statement that he was “calling for a full investigation into all potential causes” of the derailment. “The safety of New Jersey citizens is paramount, and we will do everything possible to ensure that NJ Transit and Penn Station are safe,” the statement said.

Mr. Naparstek said “the likelihood of a derailment should decrease” after Amtrak makes repairs to the tracks this summer. He said that by September, the A interlocking would be “renewed.”

Local officials have expressed doubts about Amtrak’s ability to complete the planned work by September. But Mr. Naparstek said he remained very confident that it would meet that deadline.

He added, however, that Labor Day weekend would not be the end of the work at Penn Station, only the end of the closing of multiple tracks that requires timetables to be revised. The work to repair the tracks will continue into 2018, but the long-term schedule for it will be shortened by the intensive approach.

“We’re going to compress this several years into an eight-to-10-week period, and we’re going to get it done,” Mr. Naparstek said.

But given the demands on Penn Station, where ridership has boomed beyond the capacity to easily accommodate it, constant attention will be needed.

“We will continue to do renewal work,’’ Mr. Naparstek said. “We will continue to do capacity expansion work on weekends and at night forever, probably.”

A version of this article appears in print on , on Page A1 of the New York edition with the headline: Accident Offers Stark Proof of Tracks’ Disrepair. Order Reprints | Today’s Paper | Subscribe